include ../../Makefile.conf
export HADOOP_INSTALL=${HADOOP_HOME}
jar:
	mkdir -p tmp
	mkdir -p dist
	-cp -r src/* tmp/
	${JAVAC} -d tmp/ -sourcepath tmp -cp ${HADOOP_HOME}/hadoop-${HADOOP_VERSION}-core.jar ./src/fr/cephb/mapreduce/*.java
	${JAR} cvf dist/mapreduce.jar -C tmp .
test1:jar
	rm -rf JETER
	time ${HADOOP_HOME}/bin/hadoop fr.cephb.mapreduce.CodingSnpJob ${HOME}/tmp/HADOOP/snp130CodingDbSnp.txt.gz JETER
test:jar
	rm -rf JETER
	time ${HADOOP_HOME}/bin/hadoop fr.cephb.mapreduce.ExonsJob ${HOME}/tmp/HADOOP/all_mrna.txt.gz JETER

clean:
	rm -rf tmp dist JETER
